While leaders from two Anglican schools have distanced themselves from a controversial letter defending gay discrimination exemptions, another in Waverley is under fire from former students for failing to do the same.

Key points:

School leaders of Abbotsleigh and Barker College give heartfelt apologies for distress caused by the letter

Both schools have signalled they would support reform or removal of the discrimination exemptions

Last week, the heads of 34 Anglican schools in New South Wales wrote to federal MPs urging them to protect exemptions in the Sex Discrimination Act that permitted them to sack or expel LGBTI staff and students.

Yesterday, the heads of Abbotsleigh private school for girls in Wahroonga and Barker College in Hornsby wrote to their communities, apologising for the distress the letter caused.

In response to criticism, the two school leaders signalled they would support the removal of the discrimination exemptions.

It implored the headmistresses to withdraw public support for the exemptions.

"Make no mistake," the letter said, "your denial of support for [gay] students truly is a matter of life and death".

"At best, you imply that [gay] students and staff remain at the school at your pleasure — not because they, their education, or their contribution to the community is valued or protected, but because they are, for the moment, being merely 'put up with'."

In correspondence obtained by the ABC between the letter's author and Dr Townsend, the headmistress said she empathised with their concerns but would not withdraw support for the religious exemptions.

"What I am asking for is … the right to employ staff who support Christian character and purposes of the school," she said.

"If religious schools do not have religious freedom, I would not be able to do that."

DrTownsend declined to be interviewed by the ABC.

'We are sorry', say Anglican school leaders

While St Catherine graduates said they were disappointed with their headmistress's response, other Sydney Anglican school leaders stepped up and withdrew their support for the exemptions.

"I am very sorry that some members of our community have felt discriminated against," Abbotsleigh headmistress Megan Krimmer said in a letter addressed to the Wahroonga community on Monday.

"This is something that should not happen and I apologise for the incredible hurt you have felt and are feeling."

Ms Krimmer said protection for religious freedoms being tied to exemptions in the Sex Discrimination Act was "objectionable" and she would support the removal of these exemptions.

At Barker College, chair of school council Peter Berkley also offered apologetic statements and calls for reform, but noted the furious backlash was fuelled by the media and "precipitated in a social media firestorm".

"Sadly the media reporting of these matters, and escalation on social media, has impacted our students," Mr Berkley said.

"This has hurt our young people. Some of our students thought we might actually want to expel them for being gay.